Hearts Pain, Loves Gain
by writingforthemoney
Summary: Since he left there have been some changes at the Jeffersonian marriages, children and a new chain of command, just to name a few. What will happen when Booth comes back? Will these affect him and his future with the one he loves? CHAPTER 5 now UP!
1. Hey Bones

**Hearts Pain, Loves Gain**

_**Disclaimer:**__ I don't own anyone except for the little rugrats running about (except for Russ') and Zack's girlfriend._

_**Summary:**__ Booth was reassigned! Since he left there have been some changes at the Jeffersonian marriages, children and a new chain of command, just to name a few. What will happen when Booth comes back? Will these changes affect him and his future with the one he loves? BS… BB… AH… ZOC… RS?_

_**Pairings:**__ BB, BS, AH, ZOC, RS… at least I think that Russ' girlfriends name started with an S… I don't actually, yet, use her name so we're cool!_

_**A/N:**__ Any questions just ask…_

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He'd only walked in the lab five minutes before and no one had noticed him this gave him a chance to observe, something he'd learnt to do since he'd been gone. Looking around he noticed that the décor and design of the Medico-Legal Lab of the Jeffersonian hadn't changed much in the past four years. The only thing that he saw that was different was the chain of command. Camille Soryoran was nowhere to be seen as of yet. Drs. Jack Hodgins and Zack Addy were still just as squinty as ever just by appearances and Ms. Angela Montenegro held her sketchpad in her hand as if it were the only thing she had. He smiled watching the squints hard at work and then felt his breathing catch as _she_ walked into his eye line.

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"Audrey, be good for Uncle Russ, until I get home. I won't be long, just a few more hours okay?"

The little girl whined, "But mommy he won't let me jump on my bed."

She smiled, "Sweetheart you don't need to be jumping on your bed." Through the glass she saw that Hodgins and Zack seemed to be progressing rather quickly, "Sweetie, I've gotta go. I'll be home before long. I love you."

"Mommy can I come visit you if you don't come home in a while?"

Her mother smiled through the receiver, "Audrey…."

"Pleeeease!" She begged. Brennan could almost see the puppy dog eyes and smile, just like her fathers, and she gave them the same reaction she had her father; a roll of her eyes, but conceded anyway.

"Okay, if I'm not home by five tell Uncle Russ to bring you here, so he can go home to your cousins and aunt." She sighed, "Mommy's really gotta go now okay, so I'll see you before long. I love you."

"Love you more Mommy, bye!"

She smiled as she put the receiver down, and then walked out of her office and made her way on the platform, not paying attention to anyone around her except her team.

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She was gorgeous, even more than before if it were possible. There seemed to be a glow about her, almost as if she were in love… then Sully entered his mind… The thought hit him hard, he hoped she wasn't in love with Sully, but could he expect her to have waited? He wanted her to be happy, and if she was then he would accept it.

Her back was turned toward the door of the lab speaking to the rest of her team, each facing the door, their eyes however where focused on the woman speaking. She was looking at the skeleton that lay before her whilst explaining how she died. "See here Zack, you just overlooked the…" her explanation continued.

He was starting to attract some attention so he walked to the platform and was about to swipe his pass key card (that seemed to have never left his wallet) when he remembered that the Jeffersonian would have changed security codes by now. So he spoke his first words in the now seven minutes he'd been there, "Hey Bones."

Everyone froze for a moment and then raised their heads toward the voice, that is everyone but the person it addressed. Her back went rigid, her voice ceased in a small squeak, her hands froze in mid-motion, her breathing stopped and her heart pounded faster and faster at one word; Bones. Only one person ever dared, ever dreamed and ever did call her Bones, and he'd left her four years ago; she had long since then given up on him ever coming back…until that word, that name; Bones. Her mouth involuntarily mouthed the name of her old partner; she swallowed hard and turned toward the voice.

Her breathing returned but was erratic as was her heart at the man before her. She had to restrain herself from running to him or shouting happily his name. She swallowed once more and closed her eyes trying to rid her mind and body of the images and feelings he instantly reminded her of. Clearing her throat she spoke, "You're back? Are you staying?" _Please tell me you're staying!_ Her thoughts begged.

He smiled up at her seeing all the love and memories in her eyes, "Miss me?" The question wasn't spoken in jest but was very sincere.

"Are you staying?" she avoided his question.

"Yes; I'm back…for good."

She felt as if her world was right again and she nodded mouthing to him, "Yeah, I missed you."


	2. Four Years Earlier

_Four Years Earlier…_

"Cullen, you can't be serious! I've been posted here since I started this job!" Booth practically yelled across his boss' desk. "I've got Parker, Bones…" as an after thought he added, "a-and the squints, what are they going to do?"

Cullen finally spoke, "Booth, another agent will be assigned to them—"

Booth cut him off, "You know as well as I do that Bones won't be okay with just doing the lab work. And you also know that no other agent is gonna put up with her in the field, heck it took me a few months to get used to her!"

"Booth, I know that you care about Dr. Brennan—"

"I don't _care_ about her." He mumbled as Cullen continued.

"As partners, you care about her." He rolled his eyes, an action Booth had never saw his boss do before, "I'll do my best to make sure the agent with them will involve them as much as possible."

Booth looked at him and sighed, "Do you know what agent will be taking my place?"

Cullen pulled his glasses to his eyes and looked down at the papers in front of him reading, "It says here that Agent Sullivan will be the agent –"

"Sully!" Booth shouted.

Cullen moved his glasses down off his nose, "Is there a problem Booth?"

Booth gritted his teeth, taking deep breaths, "No sir."

"Hey Bones." Booth said solemnly as he sat across from her in the chair.

Brennan looked up from her paperwork, "What's wrong Booth?"

He grinned, she may not have learned to read people but she'd learnt to read him, "I have bad news."

"What's wrong?" She asked again.

He stood and walked over to her, "Will you have dinner with me tonight? I'll tell you then what's up, okay?"

She furrowed her brows, "Okay."

When he walked out the door she picked up the phone, "Tim, I'm going to have to cancel our date tonight."

"That's fine we'll have plenty of time to reschedule."

"What do you mean by that?" She asked, thinking that it was an odd statement.

Sully smiled, "You mean you haven't heard?"

"Haven't heard what?"

"We're going to be partners!" he said excitedly.

Brennan's brows furrowed together, "What?"

When she had arrived at his apartment she smelt food cooking on the stove and heard the television on, all the while the radio was also playing; after listening for a moment she realized that Foreigner was singing. She grinned, "Booth I'm here!"

"Oh hey, didn't hear you come in."

"I wonder why?" she smiled at him, dreading what he was going to tell her.

His eyes shined, "Have a seat; supper will be done in just a minute."

They ate the delicious dinner on his couch while something on cable was being broadcast through the television. After their plates were clean she insisted upon helping with the dishes. While doing so a water fight ensued, leaving both soaked and laughing. However there seemed to be sadness behind Booth's gaiety.

They once again sit on the couch, him at the corner and her in the middle. She decided to let him tell her, she honestly wished that Tim hadn't so Booth could. "What's this bad news you were going to tell me?"

He smiled sadly at her, "I'm being reassigned."

Even though she already knew hearing it come from his mouth made her heart fall, "When? Why? Wh--?"

He took her hands in his, "Tomorrow's my last day at work, and I'm leaving the day after." He paused, "I don't know why, or how long… just that it's for a long time and not in D.C."

Her heart was beating so loud she could barely hear his words. She'd come to the realization that she was in love with the man in front of her, never mind Sully, she knew the minute she heard Booth and her would no longer be partners that it was true. She looked down at there now intertwined hands and smiled, "Booth?" She swallowed hard and looked directly into his eyes, before taking her lips to his for a mere second, "I think I love you."

The next morning she awoke in his arms and sighed at the contact and because she knew it'd be the only time she'd ever feel this way. He moved a little and kissed her cheek, "We'd better get going. I've got to tell the squints today."

At the lab they had gathered everyone into Brennan's office once Booth had arrived toward the end of the day, "Cullen has informed me that I won't be working with you anymore, in fact I won't be working in D.C. anymore."

After the goodbyes, tears and hugs from Angela and the squints Booth and Brennan were left alone in the lab, in her office. "I'll miss you." She spoke the words but didn't know where they'd come from.

He crossed the space between them and kissed her pulling her to the couch beside them. They seemed to be making up for lost time, but neither cared, they both loved the feel of each other's skin on theirs.

Brennan seemed to forget about her make up date with Sully for he was at her door knocking at seven that night. When no one answered he called her cell, no answer. He called the lab and Angela answered, "Sully…uhm…" she didn't know what to say, "I think she's spending Booth's last night with him. I believe they mentioned something about eating some take-out and watching," she laughed a little, "X-Files reruns."

Booth's last night may not have been spent exactly the way Angela had described it but Sully had left them alone, which later he would regret terribly. Booth and Brennan had made love all night and morning and when Brennan had gotten to work that afternoon at four, no one questioned her whereabouts; they left her to herself. To her thoughts about how she felt about Booth and Sully.

Brennan had kept her and Booth's affair to herself for a week while she and Sully continued whatever it was they had. Finally though she couldn't stand it any longer, "Booth and I slept together!" she blurted out, giving him no time to respond she continued to speak faster and faster, "I'm sorry, but when I found out that he was leaving, I … well…" she brought her eyes to Sully's, "We love each other… we just realized it a bit too late."

Sully didn't take it too bad, but he didn't take it well either, because he started to leave them out of certain parts of cases, like field work. Everyone knew that something had happened between the agent and anthropologist, but no one guessed what it was.

A month after Booth had left they had talked to each other a few times, but his location was still on a need to know basis, no matter who had what clearance. "I'm fine Booth, I promise." She sighed into the phone, "So you're pretty positive that you'll be wherever you are for years?"

She found herself asking this question every time they spoke and the answer was always the same, "I'm sorry Bones…I don't know and even if I did I wouldn't be able to tell you. I love you, Temperance." She returned the emotion with everything in her.

"I love you too." She paused, "Seeley, we are away from each other and will be so… I'm not expecting you to go cold turkey." She tried to hide her sniff, "Find someone to be with. I hope whoever she is will make you happy." Her tears started to fall, much to her dismay.

She knew that long distance relationships didn't work out just as much as he did, so she wasn't surprised when he'd said, "I wondered what had happened with you and Sully, now I guess I know." She didn't correct him, thinking that if he thought she'd moved on that it would help him to as well.

Brennan put the phone on the dock with tears in her eyes, she didn't know what to do (after that the calls got fewer and fewer, until one day they stopped all together). She wasn't sure what she was going to do, or who she was supposed to tell. And she defiantly didn't know how this had happened … well she knew _how_ it happened … but not how … she was always safe; no matter whom she was with.

Angela found Brennan in her office deep in thought, head in her hands, and tearstains down her cheeks, "What's wrong sweetie?"

"I'm…" Brennan was shell-shocked, as she swallowed hard looking up at Angela, "I'm pregnant…"

Angela's eyes widened excitedly, "What? Who's… I mean, does Sully know? Are you going to tell him?"

Brennan looked at her, "Why do you think it's his?"

"Have you slept with anyone else?"

She remembered then that her, Booth and Sully were the few who knew of their escapade. "Uhm…no…" she lied.

"So then it's his?" Angela reasoned. "Are you going to tell him?"

Brennan wasn't sure who the father was., so she skipped the first question with haste and answered the second in a determined, stern voice, "No, I don't want him to know yet."

"Why not?"

Brennan thought, "I don't know what I'm going to do yet." 

"What do you mean? You not seriously thinking of giving it up, not after your experiences in the system?"

"I don't know Angela! I'm not a people person! I've never really wanted kids…" Brennan was in tears again. "I just don't know… I wish..." Angela thought Brennan said Sully, but couldn't be sure because she was crying so much, "…was here."

Angela, trying to be a helpful friend smiled and stood, "I'll go call Sully…"

"No!" Brennan shouted, "No, I'll tell him when I'm ready! I'll tell him when I've decided what to do.'

"But sweetie, the father has a right to be a part of the decision process. And besides you just said you wished he was here."

"No, I said I wish Booth was here." Angela's expression she continued, "Before he left, since he walked into our lives, he always helped me talk through things," pausing she smiled, "that is after I talked them out with you."

Angela smiled. "I know I'm not as sexy as Seeley but I'm here anytime you need to talk."

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	3. Of Curls, Eyes, Smiles and Years

_**A/N:** I'm not sure about the age and the time lapse thing... but you know that it's been four years since Andrey was conceived... so if the age thing is wrong... I'm sorry, tell me and I'll fix it! Sorry ... I'm not good at the little stuff like that... or big stuff I guess just the fluff! _

_Oh and thanks for reading please review!_

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Sitting in the lounge of the lab they were getting caught up on each others lives. Brennan was made director of the Jeffersonian, but held the lead forensic anthropologist position with Zack. Angela Montenegro was now and had been for two years Angela Hodgins and Zack was dating a young woman, Amanda, he'd meet at the college he was teaching at.

Angela spoke, "And Russ and his girlfriend, do you remember her? Anyway, they were married and are now living in D.C." She smiled; "Their kids now have a cou--" she stopped speaking abruptly realizing that this was something that Brennan should tell Booth.

"Russ's kids have what?" he asked.

They all looked at each other, Brennan especially giving Angela a glare that could have rotted bone. She was about to speak when as if on cue a voice was heard coming up the steps, "Marco?"

As he stepped onto the upper deck with a hand belonging to a bundle of red-brown curls in his, Brennan looked at him, "Russ, this really isn't a good time."

Just then he noticed the man sitting beside his sister and his eyes widened, "Booth!"

Booth stood, smiling, "Hey Russ, hear you got married, she one of yours?" he pointed to the girl.

Russ looked at his sister; she shook her head telling him that Audrey hadn't come up yet. "Booth?" Brennan spoke from the couch. He turned to her, "She's our daughter."

"Who's?" He asked sitting heavily beside her.

Brennan's eyes widened hoping that he was the only one who heard her slip, "She's mine."

He looked from mother to child, still trying to figure out if he'd imagined her 'our' in the last words she spoke. "She looks just like you."

She smiled, "Mommy, is this …" she paused thinking as she walked to sit in between them, "Se, Se…the man in the picture on your desk, and the TV, and the coffee table and the bookshelf and your nightstand, and …""

She put her hand over her little girls mouth, smiling, embarrassed, at the man in question, "Yes, sweetheart, Seeley." Brennan found Booth sending her the charm smile and realized that it could still make her grin and feel as if she were on cloud nine. She then looked back at her daughter, "Remember he used to be my partner, but he had to move away on business."

"Hi." The little girl smiled up at him. She seemed to be a bit shell shocked at seeing this man right here in front of her.

"Hi! What's your name?"

She smiled a familiar smile; her fathers smile, at him, "Audrey Christine Brennan!"

Booth grinned at the girl, "I love your curls. When my son, Parker, was about your size he had curls like that." He gave her a wink and she giggled. Brennan had thought the same thing when she'd first noticed them on the girl, so did Dr. and Mrs. Hodgins, both of them teasing her about it. She had come to the silent conclusion that Booth must have also had curls when he was younger, or at the very least Parker's came from his genes.

The little girl hugged him suddenly and then jumped up, "Mommy can I go draw with Aunt Angela?"

"You'll have to ask Angela that."

"Come on sweetie," Angela jumped up from her seat, "Uncle Jack and Zack can come and help us, what do you say about that?"

The girl giggled and grabbed Jack and Zack's hand, "Come Aunt Ange!" Everyone laughed as she dragged them skipping to Angela's office.

Booth smiled and then a question fell on the tip of his tongue, "How old is she?"

Russ gave her a scolding glare, which seemed to say, 'Tell him!'

"She'll be four on Saturday."

Booth smiled slightly as he began to process things, "As I said before, she looks just like you, except her eyes." He had silent hope as he noticed the brown orbs.

"Gets them from her dad…acts just like him as well." Brennan said absently, laughing slightly.

Booth looked at her, happy to see her smile, "She said her name was Brennan, you didn't take Sully's name?"

She shook her head, "No…he's not…we never married," she thought about how to tell him this, "Her father left before she was born, he didn't even know of her existence until recently. And he still doesn't know he's the father." It wasn't a lie, it just didn't tell him the exact truth.

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**_Hit the little button and tell me what you think..._**


	4. Secrets Told, Truths Revealed

_**A/N:** Thank you all for all the feedback, I've gotten bad about not replying back to all of the reviews that you all have sent me and i'm so sorry about that! I appreciate all of the feedback. Please overlook my stressed out, final-reviewing, life for the moment and keep them coming! Thank you again!_

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Booth looked at her, happy to see her smile, "She said her name was Brennan, you didn't take Sully's name?" 

She shook her head, "No…he's not her" she let out a breath, "…we never married," she thought about how to tell him this, "Her father left before she born, he didn't even know of her existence until recently. And he still doesn't know he's the father." It wasn't a lie, just didn't tell him the exact truth.

"Sully left? Left the FBI all together or just you?" he didn't like talking about him and their relationship but if he left her, Booth felt the need to hurt him.

Brennan sighed, Booth didn't understand, "He's not Aud … yes Sully did leave the FBI…but we broke up. I broke it off before she was born," she paused, "He found out about…" she looked at him with widened eyes.

"Oh…how?"

She just noticed that Russ was still standing behind Booth, "Russ you can sit down."

He shook his head, "No, I think I'll go draw with Audrey."

Booth looked between the siblings, her eyes widened as he tightened his face as if they were trying to tell each other something. "Russ…"

"Temperance." He paused, "I'm going to go draw; you two need to talk."

Once Russ had disappeared from his view he spoke, "What was that about?"

She closed her eyes and then looked up at him, "You seem to think that Sully is the father…he's not…"

"Oh, does she know who her dad is?" he asked, hoping he knew whom it was but not wanting to ask her directly.

Brennan looked down, "We have pictures but no, she doesn't know he's her father. Or at least I haven't told her, I think she can tell though." Booth looked at her in question, and decided for now to let the coincidence of pictures slip. "I talk about him all the time and I know I smile too often when I speak of him." She paused and smiled, "And her father has this uncanny skill at reading people, she inherited it." Brennan hoped that he understood now, "She already knows _way_ too much about everyone." He nodded, smiling, as she continued, "And…the reason I ended it with Tim was because, I told him about what had happened between us…" she paused gauging his reaction, "he was still our corresponding agent until…he found out I was pregnant."

Booth shook his head, "Why? What happened? He didn't think she was mine did he?"

She looked up at him, with a sort of sad smile, as she recalled that day.

_Flashback…_

_She was standing over the remains of their current victim, not too long after she had shared her surprising news with Angela, when Sully touched her back to get her attention. She stood upright, Sully then asked, "I know a man should never ask a woman about her weight, but are you okay… you look like you've gained a little in your face…"_

_Brennan looked at him incredulously, planning on playing it off and him not find out when Angela, who must have forgotten that she was the only person in the lab who knew of their friends medical condition, spoke, "That's just baby fat!" however as soon as the words were out of her mouth she realized they weren't supposed to leave it. _

_Brennan squinted her eyes shut and awaited the comments. "Baby fat?" a voice spoke._

"_As in pregnant…?"_

_Then Sully's voice spoke for the first time, angrily, "I guess I don't need to ask who the father is, do I?" Brennan opened her eyes in time to see his retreating back going towards her office. _

"_Tim!" she ran after him, no one seemed to understand, especially not Angela she thought Sully was the dad. Once reaching her office she saw him sitting on her couch, "How do you know it's _not_ yours!?"_

_He looked up at her, hope evident in his eyes, "Is it?"_

_She straightened her shoulders, "I just got the test back this morning."_

_He eyes locked with hers for a mere second longer and then he looked down. Standing he sighed, "Are you going to tell him?"_

"That's why he left, he wasn't the father and it had been awkward anyway… so…" she coughed, "I'm not one to sleep with the next random guy I see … I only slept with…" she was mumbling and in the end couldn't make complete sentences.

He touched her hand and smiled, "Does anyone else know?"

Brennan sighed, "Russ and Sully are the only ones who I've told. That's why she goes by Brennan,"

"So you didn't keep your last name with her?"

Tempe looked at him with tears forming in her eyes, shaking her head, "I couldn't help but hope her father would come back. On her birth certificate her name is Audrey Christine Brennan Booth."

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_**I almost left it rigth after the flashback, and made you beg for the last bit... but then I remembered how rude I'd been about not replying back so, since I couldn't get you Booth and it's so very hard to get cookies through the computer screen and over the web to the right places, I settled with this conclusion. LOL. Please tell me what you think.**_


	5. Squinting at the Truth

He took a deep breath and smiled, swallowing back his tears, "I had hoped… when I saw those curls, you weren't married, the age…" he trailed off. "But, why didn't you tell me?"

She had a tear in her eye, "I … you were who-knows-where, and we didn't know how long you'd be there… I just thought it'd be best, I was wrong…"

He nodded, understanding. He suddenly chuckled, "What did Angela do when Sully left?"

She smiled, "She was furious. Every time we saw him, before he quit the FBI, she gave him a glare that killed. I told him she didn't know about you and he understood. He was really nice considering four people, two of whom, have the training and intelligence to make very dangerous weapons and or chemicals that would harm his life, were extremely angry at him."

"Four people?"

She nodded, "Cam." He hadn't seen her, and knew that Brennan had her job, "She still helps us occasionally but she works for you guys now."

Everyone was now coming back up to the lounge, Booth and Brennan looked at each other and both reached for the others hand for support or love, which ever was needed. "Look what I drew Mommy!"

She looked at the paper Audrey held up and smiled, "It's beautiful, sweetie."

"That's really good!" added Booth suddenly feeling very fatherly and his chest filled with pride as he looked at the picture; Himself, Audrey and Bones were in the forefront of the picture, while the squints were in the back, as if she'd added them at the last second.

Brennan looked back at Booth and smiled, "Audrey sweetie, will you go with your uncle to me some water to drink?"

"Okay Momma!" Russ looked at her with furrowed brows.

"I've got something I need to tell my friends." He understood and grabbed his niece's hand, taking her downstairs again.

"What do you need to tell us?" Hodgins asked.

"The truth…"

"About…" Angela asked, holding her own glass of water.

Brennan looked down for minute then back up, "Sully"s—" she was cut off.

"That low, piece of – what'd he do? Is he coming and wanting custody rights after four years!" Angela was furious, "That son of a—"

"Ange!" Booth stopped the profanity. "Let's hear what Bones has to say, okay?"

She took a breath, "Sorry sweetie, go ahead what about him?"

"He's not Audrey's father."

"What!? You told me you hadn't slept with anyone but him…?"

"I lied." She spoke bluntly.

"Well then who's the dad?" Zack asked.

Before Bones could get it out everyone received a shower as Angela's water came spitting out of her mouth, a squeal soon following. "Ange, babe, you okay?"

She nodded her head excitedly, "She's four…curly…smile…eyes…."

"Babe you're not making any since."

Brennan scooted closer to Booth, smiling, "She's trying to tell you to think. Think about Audrey's smile, her eye color, her curly hair, and her age."

Zack thought, "What about it?"

Hodgins finally spoke, "The good doctor here is trying to tell us that before he left, she and the G-man got it on."

Zack shook his head, "So Audrey is yours and Booth's daughter?"

They smiled tightening their hold on each other's hand.


End file.
